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OJBTM
Online Journal of Bioinformatics ©
Identification of
SSR-ESTs corresponding to alkaloid, phenylpropanoid and
terpenoid biosynthesis in MAP’s.
Bioinformatics
& In Silico Biology Division, Central
Institute of Medicinal & Aromatic Plants (CSIR), P.O. CIMAP, Lucknow-226015 (UP), India.
ABSTRACT
Tripathi KP, Roy
S, Khan F, Shasany AK, Sharma A, Khanuja
SPS., Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid
and terpenoid biosynthesis in MAP’s, On J Bioinform., 9 (1): 78-91, 2008. Simple sequence repeats (SSRs) are
repetitions of nucleotide motifs of 1 to 5 bases and are currently the markers
of choice in many plants and animals genomes. SSRs are the DNA regions where a
few bases are tandemly repeated. SSRs have been proven to be the markers of
choice in plants genetics research and for breeding purposes because of their
hyper-variability and ease of detection. However, development of these markers
is expensive, labour intensive and time consuming, if
they are being developed from genomic libraries. In this study, SSRs were mined
in silico from ESTs of
medicinal and aromatic plants (MAPs) corresponding to secondary metabolites
e.g. Alkaloids, Phenylpropanoids and Terpenoids. SSRs are potential candidates for markers, gene
tagging, comparative genomics research and breeding purposes. For this,
comparative genomic study was performed for finding the corresponding genes to
these SSR-ESTs using Arabidopsis
thaliana as a model organism. Results revealed that the SSRs e.g., 941 trinucleotides, 213
dinucleotides, 157 tetranucleotides and 179 pentanucleotides were distributed throughout the studied
datasets of ESTs in medicinal plants viz., Coptis
japonica, Oryza sativa, Papaver somniferum,
Catharanthus roseus, Phaseolus vulgaris, Capsicum annuum,
Mentha piperita and
Euphorbia tirucalli. Primers associated
with the SSR-ESTs were also designed successfully. Moreover, functional
perspectives of these SSRs suggest that microsatellites are more than mere
repetitive sequences and their role have been attributed to many biological
functions. Because of their abundance and high polymorphism, microsatellites
could be widely used to develop genetic markers for the construction of linkage
maps of medicinal crops.
Keywords:
ESTs, SSRs, Microsatellites, Primers, Markers, Secondary metabolites,
Alkaloids, Phenylpropanoids, Terpenoids,
Medicinal & Aromatic Plants.
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